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Add membrane tutorial with packmol-memgen setup#310

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hannahbaumann wants to merge 6 commits into
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Add membrane tutorial with packmol-memgen setup#310
hannahbaumann wants to merge 6 commits into
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packmol-example

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Colab 👈 Launch a Colab session on branch packmol-example

@hannahbaumann hannahbaumann changed the title [WIP] Add membrane tutorial with packmol-memgen setup Add membrane tutorial with packmol-memgen setup Jun 12, 2026
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@IAlibay IAlibay Jun 15, 2026

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[nit] It's ok as is, but also for a less technically minded audience, it would also be ok to just use ! to call the command line dirrectly.


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Changed this!

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@IAlibay IAlibay Jun 15, 2026

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This is great!


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@IAlibay IAlibay Jun 15, 2026

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[nit] can you add a link to the PDB standard where it defines CRYST1?


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Added this!

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@IAlibay IAlibay Jun 15, 2026

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[nit] can you expand on createStandardBonds with the underlying package/object?


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@IAlibay IAlibay Jun 15, 2026

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[nit] as above, just doing Topology.loadBondDefinitions() would be ok.


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@IAlibay IAlibay Jun 15, 2026

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[nit] can you put this in one of those warning boxes? Like we do for https://github.com/OpenFreeEnergy/ExampleNotebooks/blob/main/membranes/rbfe_membrane_protein.ipynb


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@IAlibay IAlibay Jun 15, 2026

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Line #61.    with open('a2a/complex_equ.pdb', 'w') as f:

[nit] might be good to call it "complex_equil", might just be me but "equ" is hard to parse somehow.


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Renamed this!

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@IAlibay IAlibay Jun 15, 2026

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To reduce maintenance burdens, it would be ok if the notebook finished here and just referred to another one.


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Overall lgtm, a few nits, but nothing I would consider block.

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@jthorton jthorton Jun 15, 2026

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Should this one be in the highlighted note box as well, it feels like an important one to highlight.


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Looks great!

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